School of Chemistry and Molecular Biosciences

Dr Yoochan Myung

Postdoctoral Research Fellow
School of Chemistry and Molecular Biosciences
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Publications

Book Chapters (3)
Journal Articles (22)

Book Chapters

Ascher, David B., Kaminskas, Lisa M., Myung, Yoochan and Pires, Douglas E. V. (2022). Using graph-based signatures to guide rational antibody engineering. Computer-aided antibody design. (pp. 375-397) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2609-2_21
Pires, Douglas E. V., Portelli, Stephanie, Rezende, Pâmela M., Veloso, Wandré N. P., Xavier, Joicymara S., Karmakar, Malancha, Myung, Yoochan, Linhares, João P. V., Rodrigues, Carlos H. M., Silk, Michael and Ascher, David B. (2020). A comprehensive computational platform to guide drug development using graph-based signature methods. Structural bioinformatics: methods and protocols. (pp. 91-106) New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0270-6_7
Pires, Douglas E. V., Rodrigues, Carlos H. M., Albanaz, Amanda T. S., Karmakar, Malancha, Myung, Yoochan, Xavier, Joicymara, Michanetzi, Eleni-Maria, Portelli, Stephanie and Ascher, David B. (2019). Exploring protein supersecondary structure through changes in protein folding, stability, and flexibility. Protein Supersecondary Structures: Methods and Protocols. (pp. 173-185) edited by Alexander E. Kister. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-9161-7_9

Journal Articles

AlJarf, Raghad, Rodrigues, Carlos H. M., Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2024). piscesCSM: prediction of anticancer synergistic drug combinations. Journal of Cheminformatics, 16 (1) 81. doi: 10.1186/s13321-024-00859-4
Pan, Qisheng, Parra, Georgina Becerra, Myung, Yoochan, Portelli, Stephanie, Nguyen, Thanh Binh and Ascher, David B. (2024). AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information. Protein Science, 33 (10) ARTN e5147, e5147. doi: 10.1002/pro.5147
Gu, Xiaotong, Myung, Yoochan, Rodrigues, Carlos H. M. and Ascher, David B. (2024). EFG‐CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models. Protein Science, 33 (8) e5096, e5096. doi: 10.1002/pro.5096
Zhou, Yunzhuo, Myung, YooChan, Rodrigues, Carlos H M and Ascher, David B (2024). DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning. Nucleic Acids Research, 52 (W1), W207-W214. doi: 10.1093/nar/gkae412
Gu, Xiaotong, Kovacs, Aaron S., Myung, Yoochan and Ascher, David B. (2024). Mutations in Glycosyltransferases and Glycosidases: Implications for Associated Diseases. Biomolecules, 14 (4) 497, 497. doi: 10.3390/biom14040497
Myung, Yoochan, de Sá, Alex G C and Ascher, David B (2024). Deep-PK: deep learning for small molecule pharmacokinetic and toxicity prediction. Nucleic Acids Research, 52 (W1), W469-W475. doi: 10.1093/nar/gkae254
Al-Jarf, Raghad, Karmakar, Malancha, Myung, Yoochan and Ascher, David B. (2023). Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequences. Genes, 14 (10) 1890, 1-11. doi: 10.3390/genes14101890
Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B (2023). Understanding the complementarity and plasticity of antibody–antigen interfaces. Bioinformatics, 39 (7) btad392, 1-7. doi: 10.1093/bioinformatics/btad392
Tichkule, Swapnil, Myung, Yoochan, Naung, Myo T., Ansell, Brendan R. E., Guy, Andrew J., Srivastava, Namrata, Mehra, Somya, Cacciò, Simone M, Mueller, Ivo, Barry, Alyssa E, van Oosterhout, Cock, Pope, Bernard, Ascher, David B and Jex, Aaron R (2022). VIVID: a web application for variant interpretation and visualisation in multidimensional analyses. Molecular Biology and Evolution, 39 (9) msac196. doi: 10.1093/molbev/msac196
Ruff, Kiersten M., Choi, Yoon Hee, Cox, Dezerae, Ormsby, Angelique R., Myung, Yoochan, Ascher, David B., Radford, Sheena E., Pappu, Rohit V. and Hatters, Danny M. (2022). Sequence grammar underlying the unfolding and phase separation of globular proteins. Molecular Cell, 82 (17), 3193-3208.e8. doi: 10.1016/j.molcel.2022.06.024
da Silva, Bruna Moreira, Myung, YooChan, Ascher, David B. and Pires, Douglas E. V. (2022). epitope3D: a machine learning method for conformational B-cell epitope prediction. Briefings in Bioinformatics, 23 (1) bbab423, 1-8. doi: 10.1093/bib/bbab423
Nguyen, Thanh Binh, Myung, Yoochan, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity. NAR Genomics and Bioinformatics, 3 (4) lqab109, lqab109. doi: 10.1093/nargab/lqab109
Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2021). CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function. Bioinformatics, 38 (4), 1141-1143. doi: 10.1093/bioinformatics/btab762
Lin, Heyu, Ascher, David B., Myung, Yoochan, Lamborg, Carl H., Hallam, Steven J., Gionfriddo, Caitlin M., Holt, Kathryn E. and Moreau, John W. (2021). Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The ISME Journal, 15 (6), 1810-1825. doi: 10.1038/s41396-020-00889-4
Portelli, Stephanie, Olshansky, Moshe, Rodrigues, Carlos H. M., D’Souza, Elston N., Myung, Yoochan, Silk, Michael, Alavi, Azadeh, Pires, Douglas E. V. and Ascher, David B. (2021). Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 53 (2), 254-254. doi: 10.1038/s41588-020-00775-x
Portelli, Stephanie, Myung, Yoochan, Furnham, Nicholas, Vedithi, Sundeep Chaitanya, Pires, Douglas E. V. and Ascher, David B. (2020). Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Scientific Reports, 10 (1) 18120, 1-13. doi: 10.1038/s41598-020-74648-y
Portelli, Stephanie, Olshansky, Moshe, Rodrigues, Carlos H. M., D’Souza, Elston N., Myung, Yoochan, Silk, Michael, Alavi, Azadeh, Pires, Douglas E. V. and Ascher, David B. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52 (10), 999-1001. doi: 10.1038/s41588-020-0693-3
Pires, Douglas E V, Veloso, Wandré N P, Myung, YooChan, Rodrigues, Carlos H M, Silk, Michael, Rezende, Pâmela M, Silva, Francislon, Xavier, Joicymara S, Velloso, João P L, da Silveira, Carlos H and Ascher, David B (2020). EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. Bioinformatics, 36 (14), 4200-4202. doi: 10.1093/bioinformatics/btaa480
Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2020). mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Research, 48 (W1), W125-W131. doi: 10.1093/nar/gkaa389
Myung, Yoochan, Rodrigues, Carlos H. M., Ascher, David B. and Pires, Douglas E. V. (2020). mCSM-AB2: guiding rational antibody design using graph-based signatures. Bioinformatics, 36 (5), 1453-1459. doi: 10.1093/bioinformatics/btz779
Seo, Myungwon, Shin, Hyun Kil, Myung, Yoochan, Hwang, Sungbo and No, Kyoung Tai (2020). Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development. Journal of Cheminformatics, 12 (1) 6, 1-17. doi: 10.1186/s13321-020-0410-3
Rodrigues, Carlos H. M., Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2019). mCSM-PPI2: predicting the effects of mutations on protein–protein interactions. Nucleic Acids Research, 47 (W1), W338-W344. doi: 10.1093/nar/gkz383